I am testing out the next release of survival, which involves running R CMD
check on 868
CRAN packages that import, depend or suggest it.
The survival package has a lot of data sets, most of which are non-trivial real
examples
(something I'm proud of). To save space I've bundled many of
Dear Terry
Option 2 looks the best to me. They have a relatively simple change to
make and there are only four of them.
Michael
On 16/02/2021 14:39, Therneau, Terry M., Ph.D. via R-devel wrote:
I am testing out the next release of survival, which involves running R CMD
check on 868
CRAN
Strictly speaking, I don't think this is a "corrupt" representation,
given that any APIs used to access that internal representation will
call abs() on the row count encoded within. At least, as far as I can
tell, there aren't any adverse downstream effects from having the row
names attribute
This originally came up in this dplyr issue:
https://github.com/tidyverse/dplyr/issues/5745
Where `tibble::column_to_rownames()` failed because it eventually checks
`.row_names_info(.data) > 0L` to see if there are automatic row names,
which is in line with the documentation that Kevin pointed
as.matrix.data.frame does not take the absolute value of that number:
> dPos <-
structure(list(X=101:103,201:203),class="data.frame",row.names=c(NA_integer_,+3L))
> dNeg <-
structure(list(X=101:103,201:203),class="data.frame",row.names=c(NA_integer_,-3L))
> rownames(as.matrix(dPos))
[1]
Hi all,
so I've known for a while that NROW(NULL) gives 0, where nrow(NULL) gives
an error, so I naively expected NCOL to do the same.
Of course, it does not, and is documented* (more on this in a bit) as not
doing so. For those reading without the documentation open, it gives 1.
The relevant
Hi all,
I saw several people on Japanese locale claim that, on R 4.0.4,
print() doesn't display
Japanese characters correctly. This seems to happen only on Windows
and on macOS (I
usually use Linux and I don't see this problem).
For example, in the result below, "鬼" and "外" are displayed in
On 15.02.2021 21:47, Wang, Zhu wrote:
Thanks Duncan - I am planning to submit an update, so I have to deal with the
error message.
Best,
Zhu
-Original Message-
From: Duncan Murdoch
Sent: Monday, February 15, 2021 2:45 PM
To: Wang, Zhu ; r-package-devel@r-project.org
Subject: Re:
The issue is in your .gitignore file, if you clone SIAMCAT from the
Bioconductor repo.
Please take a closer look.
Best,
Nitesh
On 2/16/21, 10:17 AM, "Bioc-devel on behalf of Jakob Wirbel"
wrote:
Hi all,
I am maintaining the SIAMCAT R package and wanted to push some updates
Hi all,
I am maintaining the SIAMCAT R package and wanted to push some updates
to the bioconductor remote. It seesm to me that I have the correct
permissions to do this and it was never a problem in the past:
ssh -T g...@git.bioconductor.org | grep SIAMCAT
R W packages/SIAMCAT
I have my
Hi,
You can update the maintainer field in the DESCRIPTION file yourself. You seem
to have access to the package.
Best,
Nitesh
On 2/8/21, 8:26 AM, "Bioc-devel on behalf of Jakob Willforss"
wrote:
Hi,
I am the maintainer of the Bioconductor package NormalyzerDE.
My
Hi,
Thanks for the update.
You will have to do a few things yourself in this process once I gave
access to the new maintainers.
You will first have to change the maintainer field in your package's
description file; then, the new maintainer will have to subscribe to the
bioc-devel mailing list.
Hi Shaimaa,
I've created a BiocCredentials account for you.
https://git.bioconductor.org/BiocCredentials/account_activation/
Please activate it and add you SSH credentials. Then you'll gain access.
Best,
Nitesh
On 2/10/21, 2:10 PM, "Bioc-devel on behalf of Shaimaa Hesham Bakr"
wrote:
The daily build system will build, check, and propagate packages only once per
day. See the top of this page for some information on timing
http://bioconductor.org/developers/how-to/troubleshoot-build-report/
>From the looks of the git.bioconductor.org repo, the changes were only pushed
Hi,
I recently pushed a bug fix to my package MSstatsTMTPTM. I bumped the version
on the RELEASE_3_12 branch to 1.0.2 and when I clone the source repo (git clone
https://git.bioconductor.org/packages/MSstatsTMTPTM) I can see the changes I
made. However, when I download the package from
Hello,
I’m running the following Github R-CMD-check workflow file on my package
repository.
https://github.com/r-lib/actions/tree/master/examples#standard-ci-workflow
It passes on 3/4 operating systems — windows-latest (release), macOS-latest
(release), ubuntu-20.04 (devel) — but fails on
Hello,
I’m running the following Github R-CMD-check workflow file on my package
repository.
https://github.com/r-lib/actions/tree/master/examples#standard-ci-workflow
It passes on 3/4 operating systems — windows-latest (release), macOS-latest
(release), ubuntu-20.04 (devel) — but fails on
The key is that libglpk.so.40 cannot be loaded.
I'm guessing that igraph was installed from the RStudio package manager as a
'binary'. The RSPM had a libglpk installed when the igraph binary was built, so
the binary package expects this library to be available. It was not on the
image where
in your package NAMESPACE do you importFrom(data.table, ".I") ?
On 2/16/21, 7:52 PM, "Bioc-devel on behalf of Alice Yue"
wrote:
Hello there,
I am working to update the flowGraph package on Bioconductor and I keep
getting an error about a missing namespace for the following code
Hi Catherine,
It looks like igraph is not installed, which RCy3 depends on. This seems
odd, because my own package categoryCompare depends on RCy3 and igraph, and
it is building fine in the Bioconductor release and dev.
I would see if you can recreate this issue locally on the Ubuntu docker
Hello there,
I am working to update the flowGraph package on Bioconductor and I keep getting
an error about a missing namespace for the following code (namely ".I" for
specifying the row in data.table):
dt <- data.table::as.data.table(vec)[ , list(list(.I)), by=vec]
a code a got from
Hello,
I have released a package vasp toBioconductor
(http://bioconductor.org/packages/vasp). Recently I had a manuscript about this
package publishedon New Physiologist
(https://nph.onlinelibrary.wiley.com/doi/10./nph.17189). However, on the
manuscript, the link to the package is
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